Seems like a common issue, if the two layers of plywood are not tight together then traffic will push the top layer down, the fastener will stay put causing the staple which was flush to appear above underlayment plain.

1/4” or 1/2” staples? I used to use 1/2” staples all the time for 1/2” underlayment. Cheaper than nails and the staple gun taxes the air compressor less so I could go faster without having to let my compressor breathe. The downside is that once or twice a year I would get a staple pop. Never had that happen with 1/4” staples and 1/4” underlayment though.

I used to use narrow crown staples for 1/4" plywood, 7/8 or 1" staples so they would not stick down and out of the layers of plywood you were fastening too and they had to have the glue on the legs. The speed at which they were hammered in would melt the glue on the legs and then it would dry and hold like iron. Removing 1/4" that was stapled could be a problem sometimes, the staples would pull through the 1/4" and have to be pulled out one at a time. Tedious work.

3/4 (length) crown staple into 1/4 MDF style underlayment over wafer board subfloor. The install was last Feb in a drive through coffee stand here in Idaho, a couple feet of snow on the ground and temps in the teens. I'm pretty sure that the building did not even have a door on it until about two weeks before install and the only heat was a portable gas unit. Is it possible that the core of the wafer subfloor was still wet and over the course of drying out that the wafers themselves walked the staples up?